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- PDB-1bob: HISTONE ACETYLTRANSFERASE HAT1 FROM SACCHAROMYCES CEREVISIAE IN C... -

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Basic information

Entry
Database: PDB / ID: 1bob
TitleHISTONE ACETYLTRANSFERASE HAT1 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH ACETYL COENZYME A
ComponentsHISTONE ACETYLTRANSFERASE
KeywordsACETYLTRANSFERASE / HISTONE ACETYLTRANSFERASE / HISTONE MODIFICATION / ACETYL COENZYME A BINDING-PROTEIN
Function / homology
Function and homology information


HATs acetylate histones / histone H4 acetyltransferase activity / subtelomeric heterochromatin formation / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / histone binding / chromosome, telomeric region / DNA repair / chromatin binding ...HATs acetylate histones / histone H4 acetyltransferase activity / subtelomeric heterochromatin formation / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / histone binding / chromosome, telomeric region / DNA repair / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Fungal HAT1, C-terminal / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus / Acetyltransferase (GNAT) family ...Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Fungal HAT1, C-terminal / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase type B catalytic subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDutnall, R.N. / Tafrov, S.T. / Sternglanz, R. / Ramakrishnan, V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Structure of the histone acetyltransferase Hat1: a paradigm for the GCN5-related N-acetyltransferase superfamily.
Authors: Dutnall, R.N. / Tafrov, S.T. / Sternglanz, R. / Ramakrishnan, V.
History
DepositionJul 2, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4163
Polymers37,5661
Non-polymers8502
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.300, 47.900, 75.700
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HISTONE ACETYLTRANSFERASE / / HAT1


Mass: 37566.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: B834 / Cellular location: NUCLEUSCell nucleus / Gene: HAT1 / Plasmid: PET13A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q12341, histone acetyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE HAT1 PROTEIN USED IN THIS STUDY CONTAINS RESIDUES 1-320 OF THE 374 RESIDUE PROTEIN. THIS IS A ...THE HAT1 PROTEIN USED IN THIS STUDY CONTAINS RESIDUES 1-320 OF THE 374 RESIDUE PROTEIN. THIS IS A CATALYTICALLY ACTIVE FRAGMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
32.5 mMHEPES1drop
40.5 mMdithiothreitol1drop
50.1 M1dropCaCl2
612 %(w/v)PEG4001reservoir
70.1 MTris-Cl1reservoir
21dropAcCoA2-fold molar excess

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.93 / Wavelength: 0.93, 0.9789
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 1, 1998
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
20.97891
ReflectionResolution: 2.3→28.9 Å / Num. obs: 193352 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.034 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.29 / Rsym value: 0.139 / % possible all: 88.3
Reflection
*PLUS
Num. obs: 18259 / Num. measured all: 193352 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.139

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3301 10.1 %RANDOM
Rwork0.204 ---
obs0.204 32524 93.6 %-
Displacement parametersBiso mean: 45.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 52 113 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.111.5
X-RAY DIFFRACTIONx_mcangle_it4.792
X-RAY DIFFRACTIONx_scbond_it5.342
X-RAY DIFFRACTIONx_scangle_it7.832.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 502 10.5 %
Rwork0.315 4300 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAMETER.ELEMENTSCA.TOP
X-RAY DIFFRACTION4ACO.PARACO.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor obs: 0.315

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